#!/bin/sh
###
### Job name
#SBATCH --job-name=illumina
### Name of queue to submit to
###SBATCH --partition killing
### Time limit of total run time of the job
###SBATCH --time=20:00:00
### Number of processor cores
#SBATCH -n 40
#SBATCH --error=slurm-%j.err
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=ams@bio.aau.dk
### The actual job execution

python /pack/qiime-1.3.0/bin/pick_otus.py -i ./data/A4-08_AAACTTGA_L004_R1_001.fasta -o ./uclust_refC/uclust_ref_picked_otus -r /user/ams/data/gg_4feb2011/repsets/gg_97_otus_4feb2011.fasta -m uclust_ref --suppress_new_clusters --save_uc_files

python /pack/qiime-1.3.0/bin/make_otu_table.py -i ./uclust_refC/uclust_ref_picked_otus/A4-08_AAACTTGA_L004_R1_001_otus.txt -t /user/ams/data/gg_4feb2011/tax/greengenes_tax_genus.txt -o ./uclust_refC/uclust_ref_picked_otus/otu_table.txt 
